Author Report for: Hoegger PJNo contact information in database for Hoegger PJ
Stajich JE, Wilke SK, Ahren D, Au CH, Birren BW, Borodovsky M, Burns C, Canback B, Casselton LA and Pukkila PJ <39 more author(s)> Stajich JE, Wilke SK, Ahren D, Au CH, Birren BW, Borodovsky M, Burns C, Canback B, Casselton LA, Cheng CK, Deng J, Dietrich FS, Fargo DC, Farman ML, Gathman AC, Goldberg J, Guigo R, Hoegger PJ, Hooker JB, Huggins A, James TY, Kamada T, Kilaru S, Kodira C, Kues U, Kupfer D, Kwan HS, Lomsadze A, Li W, Lilly WW, Ma LJ, Mackey AJ, Manning G, Martin F, Muraguchi H, Natvig DO, Palmerini H, Ramesh MA, Rehmeyer CJ, Roe BA, Shenoy N, Stanke M, Ter-Hovhannisyan V, Tunlid A, Velagapudi R, Vision TJ, Zeng Q, Zolan ME, Pukkila PJ (- 39) Ref: Proc Natl Acad Sci U S A, 107:11889, 2010 : PubMed ESTHER: Stajich_2010_Proc.Natl.Acad.Sci.U.S.A_107_11889 PubMedSearch: Stajich 2010 Proc.Natl.Acad.Sci.U.S.A 107 11889 PubMedID: 20547848 Gene_locus related to this paper: copc7-a8n2b8, copc7-a8n3e0, copc7-a8n3e1, copc7-a8n6a5, copc7-a8n8h4, copc7-a8n702, copc7-a8n941, copc7-a8nkc7, copc7-a8nll5, copc7-a8nll6, copc7-a8nqf4, copc7-a8nqg3, copc7-a8nqv8, copc7-a8nvb5, copc7-a8nwm2, copc7-a8nz18, copc7-a8p0p4, copc7-d6rlx1, copc7-d6rnh7, copc7-kex1, copci-b9u444, copc7-a8nb05, copc7-a8nha0, copci-b9u443, copc7-a8nq30, copc7-a8nh79, copc7-d6rm78, copc7-a8nzs7, copc7-axe1 Abstract The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 10(8) synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes. Meiotic recombination rates vary greatly along the chromosomes, and retrotransposons are absent in large regions of the genome with low levels of meiotic recombination. Single-copy genes with identifiable orthologs in other basidiomycetes are predominant in low-recombination regions of the chromosome. In contrast, paralogous multicopy genes are found in the highly recombining regions, including a large family of protein kinases (FunK1) unique to multicellular fungi. Analyses of P450 and hydrophobin gene families confirmed that local gene duplications drive the expansions of paralogous copies and the expansions occur in independent lineages of Agaricomycotina fungi. Gene-expression patterns from microarrays were used to dissect the transcriptional program of dikaryon formation (mating). Several members of the FunK1 kinase family are differentially regulated during sexual morphogenesis, and coordinate regulation of adjacent duplications is rare. The genomes of C. cinerea and Laccaria bicolor, a symbiotic basidiomycete, share extensive regions of synteny. The largest syntenic blocks occur in regions with low meiotic recombination rates, no transposable elements, and tight gene spacing, where orthologous single-copy genes are overrepresented. The chromosome assembly of C. cinerea is an essential resource in understanding the evolution of multicellularity in the fungi. Title: Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT and Cullen D <43 more author(s)> Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT, Kersten P, Hammel KE, Vanden Wymelenberg A, Gaskell J, Lindquist E, Sabat G, Bondurant SS, Larrondo LF, Canessa P, Vicuna R, Yadav J, Doddapaneni H, Subramanian V, Pisabarro AG, Lavin JL, Oguiza JA, Master E, Henrissat B, Coutinho PM, Harris P, Magnuson JK, Baker SE, Bruno K, Kenealy W, Hoegger PJ, Kues U, Ramaiya P, Lucas S, Salamov A, Shapiro H, Tu H, Chee CL, Misra M, Xie G, Teter S, Yaver D, James T, Mokrejs M, Pospisek M, Grigoriev IV, Brettin T, Rokhsar D, Berka R, Cullen D (- 43) Ref: Proc Natl Acad Sci U S A, 106:1954, 2009 : PubMed ESTHER: Martinez_2009_Proc.Natl.Acad.Sci.U.S.A_106_1954 PubMedSearch: Martinez 2009 Proc.Natl.Acad.Sci.U.S.A 106 1954 PubMedID: 19193860 Gene_locus related to this paper: pospm-b8p1f3, pospm-b8p2q7, pospm-b8p4n0, pospm-b8p4n9, pospm-b8p5g9, pospm-b8p5r9, pospm-b8p6h2, pospm-b8p7b1, pospm-b8p7c4, pospm-b8p8w7, pospm-b8p9j1, pospm-b8p164, pospm-b8p280, pospm-b8p423.1, pospm-b8p423.2, pospm-b8p858, pospm-b8pam2, pospm-b8pam5, pospm-b8pb68, pospm-b8pbm3, pospm-b8pc54, pospm-b8pc56, pospm-b8pce4, pospm-b8pd91, pospm-b8pdk6, pospm-b8ph32, pospm-b8ph43, pospm-b8phc9, pospm-b8php7, pospm-b8phy5, pospm-b8pjg8, pospm-b8pji9, pospm-b8plr5, pospm-b8pmk3, pospm-b8pfg0, pospm-b8pg35, pospm-b8pa20.1, pospm-b8pa20.2, pospm-b8p4g8, pospm-b8phn6 Abstract Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome, and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a single putative beta-1-4 endoglucanase were expressed at high levels relative to glucose-grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Also up-regulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H(2)O(2). These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H(2)O(2) react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons with the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost. Title: The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis Martin F, Aerts A, Ahren D, Brun A, Danchin EG, Duchaussoy F, Gibon J, Kohler A, Lindquist E and Grigoriev IV <58 more author(s)> Martin F, Aerts A, Ahren D, Brun A, Danchin EG, Duchaussoy F, Gibon J, Kohler A, Lindquist E, Pereda V, Salamov A, Shapiro HJ, Wuyts J, Blaudez D, Buee M, Brokstein P, Canback B, Cohen D, Courty PE, Coutinho PM, Delaruelle C, Detter JC, Deveau A, Difazio S, Duplessis S, Fraissinet-Tachet L, Lucic E, Frey-Klett P, Fourrey C, Feussner I, Gay G, Grimwood J, Hoegger PJ, Jain P, Kilaru S, Labbe J, Lin YC, Legue V, Le Tacon F, Marmeisse R, Melayah D, Montanini B, Muratet M, Nehls U, Niculita-Hirzel H, Oudot-Le Secq MP, Peter M, Quesneville H, Rajashekar B, Reich M, Rouhier N, Schmutz J, Yin T, Chalot M, Henrissat B, Kues U, Lucas S, Van de Peer Y, Podila GK, Polle A, Pukkila PJ, Richardson PM, Rouze P, Sanders IR, Stajich JE, Tunlid A, Tuskan G, Grigoriev IV (- 58) Ref: Nature, 452:88, 2008 : PubMed ESTHER: Martin_2008_Nature_452_88 PubMedSearch: Martin 2008 Nature 452 88 PubMedID: 18322534 Gene_locus related to this paper: lacbs-b0cns1, lacbs-b0cpl4, lacbs-b0cr62, lacbs-b0cr66, lacbs-b0csq9, lacbs-b0ct56, lacbs-b0ctt5, lacbs-b0cuw1, lacbs-b0cv23, lacbs-b0cxm7, lacbs-b0cz37, lacbs-b0czx3, lacbs-b0d0z5, lacbs-b0d4i0, lacbs-b0d4j3, lacbs-b0d5n6, lacbs-b0d8k0, lacbs-b0d263, lacbs-b0dhh1, lacbs-b0dkp6, lacbs-b0dmr2, lacbs-b0dmt4, lacbs-b0dsx5, lacbs-b0dt05, lacbs-b0dtw4, lacbs-b0du88, lacbs-b0dsl6 Abstract Mycorrhizal symbioses--the union of roots and soil fungi--are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants. Boreal, temperate and montane forests all depend on ectomycorrhizae. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains approximately 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity. | |||||||
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